Fluorescent Pyrimidine Ribonucleotide: Synthesis, Enzymatic Incorporation, and Utilization.
From: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, USA.
Journal of the American Chemical Society
- Publish Date: Feb 2007
- ISSN: 0002-7863
- Volume: 129
- Issue: 7
- Pages: 2044-53
- Medium: Print
- Language: English
- Citation (JAMA): Srivatsan Seergazhi G, Tor Yitzhak, et al. Fluorescent Pyrimidine Ribonucleotide: Synthesis, Enzymatic Incorporation, and Utilization.. J. Am. Chem. Soc. Feb 2007;129:2044-53
Abstract
Fluorescent nucleobase analogues that respond to changes in their microenvironment are valuable for studying RNA structure, dynamics, and recognition. The most commonly used fluorescent ribonucleoside is 2-aminopurine, a highly responsive purine analogue. Responsive isosteric fluorescent pyrimidine analogues are, however, rare. Appending five-membered aromatic heterocycles at the 5-position on a pyrimidine core has recently been found to provide a family of responsive fluorescent nucleoside analogues with emission in the visible range. To explore the potential utility of this chromophore for studying RNA-ligand interactions, an efficient incorporation method is necessary. Here we describe the synthesis of the furan-containing ribonucleoside and its triphosphate, as well as their basic photophysical characteristics. We demonstrate that T7 RNA polymerase accepts this fluorescent ribonucleoside triphosphate as a substrate in in vitro transcription reactions and very efficiently incorporates it into RNA oligonucleotides, generating fluorescent constructs. Furthermore, we utilize this triphosphate for the enzymatic preparation of a fluorescent bacterial A-site, an RNA construct of potential therapeutic utility. We show that the binding of this RNA target to aminoglycoside antibiotics, its cognate ligands, can be effectively monitored by fluorescence spectroscopy. These observations are significant since isosteric emissive U derivatives are scarce and the trivial synthesis and effective enzymatic incorporation of the furan-containing U triphosphate make it accessible to the biophysical community.
Mesh Headings (Keywords): Aminoglycosides, Binding Sites, Fluorescent Dyes, Furans, Nucleic Acid Conformation, Pyrimidine Nucleotides, RNA, RNA, Messenger, Ribonucleotides, Spectrometry, Fluorescence, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Check for Full Text / PubMed Unique Identifier (PMID): 17256858
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